Global detection of human variants and isoforms by deep proteome sequencing

An average shotgun proteomics experiment detects approximately 10,000 human proteins from a single sample. However, individual proteins are typically identified by peptide sequences representing a small fraction of their total amino acids. Hence, an average shotgun experiment fails to distinguish different protein variants and isoforms. Deeper proteome sequencing is therefore required for the global discovery of protein isoforms. Using six different human cell lines, six proteases, deep fractionation and three tandem mass spectrometry fragmentation methods, we identify a million unique peptides from 17,717 protein groups, with a median sequence coverage of approximately 80%. Direct comparison with RNA…

• UO
  University of Toronto
• M
  Max-Planck-Gesellschaft
• NI
  National Institutes of Health

  Awards: T32HG002760, R35GM118110
• NI
  National Institute of General Medical Sciences

  Award: R35GM118110